Q07YZ9 (Q07YZ9_SHEFN) Unreviewed, UniProtKB/TrEMBL

Names and origin

Protein names

Recommended name:
Pyridoxine 5'-phosphate synthase HAMAP-Rule MF_00279
Short name=PNP synthase HAMAP-Rule MF_00279
EC=2.6.99.2 HAMAP-Rule MF_00279

Gene names

Name:	pdxJ HAMAP-Rule MF_00279
Ordered Locus Names:	Sfri_2926

Organism

Shewanella frigidimarina (strain NCIMB 400) [Complete proteome] [HAMAP] EMBL ABI72765.1

Taxonomic identifier

318167 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Alteromonadales › Shewanellaceae › Shewanella › Shewanella frigidimarina

Protein attributes

Sequence length	265 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

General annotation (Comments)

Function	Catalyzes the complicated ring closure reaction between the two acyclic compounds 1-deoxy-D-xylulose-5-phosphate (DXP) and 3-amino-2-oxopropyl phosphate (1-amino-acetone-3-phosphate or AAP) to form pyridoxine 5'-phosphate (PNP) and inorganic phosphate By similarity. HAMAP-Rule MF_00279
Catalytic activity	1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = pyridoxine 5'-phosphate + phosphate + 2 H2O. HAMAP-Rule MF_00279
Pathway	Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis; pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 5/5. HAMAP-Rule MF_00279
Subunit structure	Homooctamer; tetramer of dimers By similarity. HAMAP-Rule MF_00279
Subcellular location	Cytoplasm By similarity HAMAP-Rule MF_00279.
Sequence similarities	Belongs to the PNP synthase family. HAMAP-Rule MF_00279

Ontologies

Keywords
Biological process	Pyridoxine biosynthesis HAMAP-Rule MF_00279
Cellular component	Cytoplasm HAMAP-Rule MF_00279
Molecular function	Transferase HAMAP-Rule MF_00279
Technical term	Complete proteome
Gene Ontology (GO)
Biological_process	pyridoxine biosynthetic process Inferred from electronic annotation. Source: HAMAP
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	pyridoxine 5'-phosphate synthase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Regions
	Region	31 – 32	2	1-deoxy-D-xylulose 5-phosphate binding By similarity HAMAP-Rule MF_00279
	Region	235 – 236	2	3-amino-2-oxopropyl phosphate binding By similarity HAMAP-Rule MF_00279
Sites
	Active site	65	1	Proton acceptor By similarity HAMAP-Rule MF_00279
	Active site	92	1	Proton acceptor By similarity HAMAP-Rule MF_00279
	Active site	213	1	Proton donor By similarity HAMAP-Rule MF_00279
	Binding site	29	1	3-amino-2-oxopropyl phosphate By similarity HAMAP-Rule MF_00279
	Binding site	40	1	3-amino-2-oxopropyl phosphate By similarity HAMAP-Rule MF_00279
	Binding site	67	1	1-deoxy-D-xylulose 5-phosphate By similarity HAMAP-Rule MF_00279
	Binding site	72	1	1-deoxy-D-xylulose 5-phosphate By similarity HAMAP-Rule MF_00279
	Binding site	122	1	1-deoxy-D-xylulose 5-phosphate By similarity HAMAP-Rule MF_00279
	Binding site	214	1	3-amino-2-oxopropyl phosphate; via amide nitrogen By similarity HAMAP-Rule MF_00279
	Site	173	1	Transition state stabilizer By similarity HAMAP-Rule MF_00279

Sequences

	Sequence		Length	Mass (Da)
	Q07YZ9 [UniParc]. Last modified October 31, 2006. Version 1. Checksum: FDBA3083A06FA9B3	FASTA	265	29,093
	10 20 30 40 50 60 MHNFGYHVPH CVIYYLKELD VSGILLGINI DHIATLRQAR GTHYPDPVHA AAVAEHAGAD 70 80 90 100 110 120 GITIHLREDR RHIQDRDVYL LAKTLKTRMN FEFAVTEEMI AIACDIKPAY ACLVPEKREE 130 140 150 160 170 180 LTTEGGLDVA GQLDKIRSAV TRLAAEGIKV SLFIDADKTQ IDAAVLSGAP YIEIHTGCYA 190 200 210 220 230 240 DAITDAEQAD ELVRITEMAQ YAHSKGLVVN AGHGLHYHNV KAIAAIPELY ELNIGHAVIA 250 260 RAAIDGLDTA VRDMKKLMLE GRRGE

References

[1]

"Complete sequence of Shewanella frigidimarina NCIMB 400." US DOE Joint Genome Institute Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Fredrickson J.K., Kolker E., McCuel L.A., DiChristina T., Nealson K.H., Newman D., Tiedje J.M. , Zhou J., Romine M.F., Culley D.E., Serres M., Chertkov O., Brettin T., Bruce D., Han C., Tapia R., Gilna P., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Richardson P. Submitted (AUG-2006) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: NCIMB 400.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000447 Genomic DNA. Translation: ABI72765.1.
RefSeq	YP_751604.1. NC_008345.1.
3D structure databases
ProteinModelPortal	Q07YZ9.
SMR	Q07YZ9. Positions 24-262.
ModBase	Search...
Protein-protein interaction databases
STRING	318167.Sfri_2926.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	ABI72765; ABI72765; Sfri_2926.
GeneID	4279831.
KEGG	sfr:Sfri_2926.
PATRIC	23499985. VBISheFri14343_3034.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0854.
HOGENOM	HOG000258094.
KO	K03474.
OMA	LHYHNVK.
ProtClustDB	PRK05265.
Enzyme and pathway databases
BioCyc	SFRI318167:GIXS-3039-MONOMER.
UniPathway	UPA00244; UER00313.
Family and domain databases
Gene3D	3.20.20.70. 1 hit.
HAMAP	MF_00279. PdxJ.
InterPro	IPR013785. Aldolase_TIM. IPR004569. PyrdxlP_synth_PdxJ. [Graphical view]
Pfam	PF03740. PdxJ. 1 hit. [Graphical view]
SUPFAM	SSF63892. PyrdxlP_synth_PdxJ. 1 hit.
TIGRFAMs	TIGR00559. pdxJ. 1 hit.
ProtoNet	Search...

Entry information

Entry name

Q07YZ9_SHEFN

Accession

Primary (citable) accession number: Q07YZ9

Entry history

Integrated into UniProtKB/TrEMBL:	October 31, 2006
Last sequence update:	October 31, 2006
Last modified:	May 1, 2013
This is version 49 of the entry and version 1 of the sequence. [Complete history]

Entry status

Unreviewed (UniProtKB/TrEMBL)